SPATA12

spermatogenesis associated 12

Basic information

Region (hg38): 3:57060664-57075432

Links

ENSG00000186451 ∙ NCBI:353324 ∙ OMIM:609869 ∙ HGNC:23221 ∙ Uniprot:Q7Z6I5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA12 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	2	0

Variants in SPATA12

This is a list of pathogenic ClinVar variants found in the SPATA12 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-57073730-A-G			Likely benign (Dec 01, 2022)
3-57073783-T-A		not specified	Uncertain significance (Jan 02, 2024)
3-57073838-C-A		not specified	Uncertain significance (Nov 13, 2024)
3-57073869-G-A		not specified	Uncertain significance (Jan 18, 2025)
3-57073881-G-A		not specified	Uncertain significance (Oct 16, 2023)
3-57074010-T-A		not specified	Uncertain significance (Feb 23, 2023)
3-57074106-G-A		not specified	Uncertain significance (Jun 30, 2022)
3-57074131-G-A		not specified	Uncertain significance (Oct 14, 2023)
3-57074134-T-C		not specified	Uncertain significance (Feb 10, 2022)
3-57074167-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-57074184-A-G		not specified	Likely benign (Sep 21, 2023)
3-57074241-A-C		not specified	Uncertain significance (Nov 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA12	protein_coding	protein_coding	ENST00000334325	1	14992

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.135	103	99.2	1.04	0.00000461	1216
Missense in Polyphen		12	13.188	0.90992		146
Synonymous	0.0863	40	40.7	0.983	0.00000198	408
Loss of Function

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish
East Asian
Finnish
European (Non-Finnish)
Middle Eastern
South Asian
Other

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.322
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0606
• hipred: N
• hipred_score: 0.123
• ghis: 0.395

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.155

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium